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Pectobacterium parvum sp. nov., having a Salmonella SPI-1-like Type III secretion system and low virulence

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Abstract
Pectobacterium strains isolated from potato stems in Finland, Poland and the Netherlands were subjected to polyphasic analyses to characterize their genomic and phenotypic features. Phylogenetic analysis based on 382 core proteins showed that the isolates clustered closest to Pectobacterium polaris but could be divided into two clades. Average nucleotide identity (ANI) analysis revealed that the isolates in one of the clades included the P. polaris type strain, whereas the second clade was at the border of the species P. polaris with a 96 % ANI value. In silico genome-to-genome comparisons between the isolates revealed values below 70%, patristic distances based on 1294 core proteins were at the level observed between closely related Pectobacterium species, and the two groups of bacteria differed in genome size, G+C content and results of amplified fragment length polymorphism and Biolog analyses. Comparisons between the genomes revealed that the isolates of the atypical group contained SPI-1-type Type III secretion island and genes coding for proteins known for toxic effects on nematodes or insects, and lacked many genes coding for previously characterized virulence determinants affecting rotting of plant tissue by soft rot bacteria. Furthermore, the atypical isolates could be differentiated from P. polaris by their low virulence, production of antibacterial metabolites and a citrate-negative phenotype. Based on the results of a polyphasic approach including genome-to-genome comparisons, biochemical and virulence assays, presented in this report, we propose delineation of the atypical isolates as a novel species Pectobacterium parvum, for which the isolate s0421T (CFBP 8630T=LMG 30828T) is suggested as a type strain.
Keywords
Ecology, Evolution, Behavior and Systematics, Microbiology, General Medicine, Pectobacterium, Pectobacterium parvum, Salmonella SPI-1 T3SS, potato, soft rot, virulence

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MLA
Pasanen, Miia, et al. “Pectobacterium Parvum Sp. Nov., Having a Salmonella SPI-1-like Type III Secretion System and Low Virulence.” INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, vol. 70, no. 4, 2020, pp. 2440–48, doi:10.1099/ijsem.0.004057.
APA
Pasanen, M., Waleron, M., Schott, T., Cleenwerck, I., Misztak, A., Waleron, K., … Pirhonen, M. (2020). Pectobacterium parvum sp. nov., having a Salmonella SPI-1-like Type III secretion system and low virulence. INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, 70(4), 2440–2448. https://doi.org/10.1099/ijsem.0.004057
Chicago author-date
Pasanen, Miia, Malgorzata Waleron, Thomas Schott, Ilse Cleenwerck, Agnieszka Misztak, Krzysztof Waleron, Leighton Pritchard, et al. 2020. “Pectobacterium Parvum Sp. Nov., Having a Salmonella SPI-1-like Type III Secretion System and Low Virulence.” INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY 70 (4): 2440–48. https://doi.org/10.1099/ijsem.0.004057.
Chicago author-date (all authors)
Pasanen, Miia, Malgorzata Waleron, Thomas Schott, Ilse Cleenwerck, Agnieszka Misztak, Krzysztof Waleron, Leighton Pritchard, Ramadan Bakr, Yeshitila Degefu, Jan van der Wolf, Peter Vandamme, and Minna Pirhonen. 2020. “Pectobacterium Parvum Sp. Nov., Having a Salmonella SPI-1-like Type III Secretion System and Low Virulence.” INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY 70 (4): 2440–2448. doi:10.1099/ijsem.0.004057.
Vancouver
1.
Pasanen M, Waleron M, Schott T, Cleenwerck I, Misztak A, Waleron K, et al. Pectobacterium parvum sp. nov., having a Salmonella SPI-1-like Type III secretion system and low virulence. INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY. 2020;70(4):2440–8.
IEEE
[1]
M. Pasanen et al., “Pectobacterium parvum sp. nov., having a Salmonella SPI-1-like Type III secretion system and low virulence,” INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, vol. 70, no. 4, pp. 2440–2448, 2020.
@article{8663286,
  abstract     = {Pectobacterium strains isolated from potato stems in Finland, Poland and the Netherlands were subjected to polyphasic analyses to characterize their genomic and phenotypic features. Phylogenetic analysis based on 382 core proteins showed that the isolates clustered closest to Pectobacterium polaris but could be divided into two clades. Average nucleotide identity (ANI) analysis revealed that the isolates in one of the clades included the P. polaris type strain, whereas the second clade was at the border of the species P. polaris with a 96 % ANI value. In silico genome-to-genome comparisons between the isolates revealed values below 70%, patristic distances based on 1294 core proteins were at the level observed between closely related Pectobacterium species, and the two groups of bacteria differed in genome size, G+C content and results of amplified fragment length polymorphism and Biolog analyses. Comparisons between the genomes revealed that the isolates of the atypical group contained SPI-1-type Type III secretion island and genes coding for proteins known for toxic effects on nematodes or insects, and lacked many genes coding for previously characterized virulence determinants affecting rotting of plant tissue by soft rot bacteria. Furthermore, the atypical isolates could be differentiated from P. polaris by their low virulence, production of antibacterial metabolites and a citrate-negative phenotype. Based on the results of a polyphasic approach including genome-to-genome comparisons, biochemical and virulence assays, presented in this report, we propose delineation of the atypical isolates as a novel species Pectobacterium parvum, for which the isolate s0421T (CFBP 8630T=LMG 30828T) is suggested as a type strain.},
  author       = {Pasanen, Miia and Waleron, Malgorzata and Schott, Thomas and Cleenwerck, Ilse and Misztak, Agnieszka and Waleron, Krzysztof and Pritchard, Leighton and Bakr, Ramadan and Degefu, Yeshitila and van der Wolf, Jan and Vandamme, Peter and Pirhonen, Minna},
  issn         = {1466-5026},
  journal      = {INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY},
  keywords     = {Ecology,Evolution,Behavior and Systematics,Microbiology,General Medicine,Pectobacterium,Pectobacterium parvum,Salmonella SPI-1 T3SS,potato,soft rot,virulence},
  language     = {eng},
  number       = {4},
  pages        = {2440--2448},
  title        = {Pectobacterium parvum sp. nov., having a Salmonella SPI-1-like Type III secretion system and low virulence},
  url          = {http://dx.doi.org/10.1099/ijsem.0.004057},
  volume       = {70},
  year         = {2020},
}

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